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Refactor variant and genotype annotations #90

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merged 1 commit into from Jul 18, 2016
Merged

Refactor variant and genotype annotations #90

merged 1 commit into from Jul 18, 2016

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heuermh
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@heuermh heuermh commented Jul 7, 2016 •
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Fixes #89

Also includes style fixes, removes used Base enum, and removes unused sample fields.

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This was referenced Jul 7, 2016
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fnothaft
fnothaft reviewed Jul 11, 2016
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src/main/resources/avro/bdg.avdl
union { null, float } phylop = null;
union { null, string } ancestralAllele = null;
/**
Allele frequency, VCF INFO header line reserved key AF.
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A random note: we should name this either major or minor allele frequency.

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Also, I looked this up and VCF AF is minor allele frequency.

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Thanks, will update the doc

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@fnothaft fnothaft merged commit 5e81a9c into bigdatagenomics:master Jul 18, 2016
@heuermh heuermh deleted the annotations branch July 18, 2016 21:58
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heuermh commented Jul 18, 2016

Thanks!

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Merged! Thanks @heuermh!

@heuermh heuermh mentioned this pull request Jul 26, 2016
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fnothaft added a commit to fnothaft/bdg-formats that referenced this pull request Aug 24, 2016
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Revert "Refactor variant and genotype annotations (bigdatagenomics#90)"
7f2b6f0 
This reverts commit 5e81a9c.
heuermh pushed a commit that referenced this pull request Aug 24, 2016
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Revert back to 0.9.0 (#99)
b457b71 
* Revert "Complete refactoring of variant and related annotation records"

This reverts commit d77823d.

* Revert "Refactor variant and genotype annotations (#90)"

This reverts commit 5e81a9c.

* Revert "Use separate filtersFailed and filtersPassed arrays for variant quality filters (#88)"

This reverts commit 7b69079.
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Streamline genotype/variant annotations
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@heuermh @AmplabJenkins @fnothaft